WO2021013040A1 - 基于微孔阵列芯片的数字pcr扩增装置和利用其进行扩增的方法 - Google Patents
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/686—Polymerase chain reaction [PCR]
Definitions
- the invention belongs to the field of nucleic acid detection, and particularly relates to a digital PCR detection method based on a micropore array chip.
- Digital PCR can use large-scale parallel PCR amplification to extract weak amplification signals from background noise, and count the number of amplified molecules by "presence or absence of end-point signal”. So far, a variety of dPCR devices have been developed, mainly including well plate type and droplet type.
- the well-plate dPCR is to discretize nucleic acid molecules on a plate with a sufficient number of microwell arrays of the same size to realize digital amplification.
- the QuantStudioTM 3D dPCR system launched by ThermoFisher adopts this method. It etches up to 20,000 hexagonal micro-holes on a square plate with a side length of 10mm, each with a volume of 0.8nL, which realizes isolation between the micro-holes. By simply painting and loading, each micro-hole has about 1 target Nucleic acid molecules: After PCR, the fluorescence signal in the well can be detected, and the number of target molecules can be calculated by Poisson distribution.
- the droplet dPCR uses tens of thousands of monodisperse droplets to divide the sample.
- the droplets use hydrophobic pipes and oil phase liquids to disperse DNA with each water-in-oil droplet.
- one droplet It contains only one DNA molecule; after DNA amplification, it can be transferred to a fluorescence detection device for final detection.
- the disadvantage of this method is that the droplets are likely to merge with each other during the PCR process or the transfer process, resulting in inaccurate results.
- an object of the present invention is to provide a digital PCR amplification device based on a microwell array chip and a method for amplification using the same.
- the digital PCR amplification device has the advantages of high detection sensitivity, high accuracy and low cost.
- the present invention provides a digital PCR amplification device based on a microwell array chip.
- the digital PCR amplification device includes: a microwell array chip.
- the microwell array chip includes:
- a sealing cover the sealing cover being placed above the bottom plate for sealing each microwell in the microwell array
- a plurality of biochemical sensors one biochemical sensor is arranged in each microwell in the microwell array, and a capture probe is arranged on the surface of the biochemical sensor, and the capture probe is suitable for capturing the in the microwell Target nucleic acid and generate electrical signals;
- An electrode the electrode being adapted to provide a voltage to the solution in the micropore.
- the biochemical sensor of the digital PCR amplification device of the above embodiment of the present invention captures the amplified target nucleic acid molecule through the capture probe provided on its surface, and replaces it with the electronic detection method that detects the inherent negative charge of the nucleic acid molecule.
- the above-mentioned device of the present application can significantly reduce the complexity, volume and price of the system.
- the present invention can greatly reduce the volume of micropores (which can be reduced to 1 fL to 10 pL), thereby significantly reducing the minimum reagent usage and the price of consumables.
- the digital PCR amplification device based on the microwell array chip according to the above embodiment of the present invention may also have the following additional technical features:
- the electrode includes at least one of an on-chip electrode, a solution electrode, and an external electrode, wherein the on-chip electrode or the solution electrode is disposed on the bottom plate.
- the biochemical sensor is one of ion-sensitive field effect transistors, carbon nanotubes, silicon nanowires, graphene or molybdenum disulfide transistor sensors, or a miniature electrochemical sensor.
- the surface of the biochemical sensor is provided with a passivation layer, the passivation layer is formed on the inner wall of the micropore, and the capture probe is arranged on the surface of the passivation layer .
- the passivation layer is a stack of one or more of gold, aluminum oxide, hafnium dioxide, titanium dioxide, tantalum pentoxide, silicon dioxide, and silicon carbide.
- 1 to 1 million capture probes are provided on the surface of each biochemical sensor.
- a reading device which is electrically connected to a computer, so as to realize the electrical signal of the biochemical sensor in the microwell before and after PCR amplification of the microwell array chip Read.
- the reading device includes:
- a base, a groove for accommodating the microwell array chip is formed on the upper surface of the base, and a metal probe is arranged in the bottom wall of the groove, and the metal probe is suitable for interacting with the microwell array
- the pin pad of the chip forms an electrical connection, so as to realize the power supply to the micropore array chip and the data reading of the electrical signal of the biochemical sensor;
- a circuit board the circuit board is arranged on the lower surface of the base, the circuit board includes a data acquisition module, an ADC chip, and a processor connected in sequence, wherein,
- the data collection module is connected to the metal probe and is suitable for collecting electrical signals of the biochemical sensor
- the electrical signal is delivered to the ADC chip, and the ADC chip performs analog-to-digital conversion;
- the electrical signal after the analog-to-digital conversion is sent to the processor, and the processor performs digital signal processing and calculates the concentration of amplified DNA;
- the upper cover one side edge of the upper cover is hinged to the edge of the base, and is used to cover the base.
- the reading device includes:
- a plug-in circuit board includes a storage compartment for accommodating a micro-hole array chip, a cover placed at the mouth of the storage compartment, and a signal for amplifying the biochemical sensor signal on the micro-hole array chip Amplifier chip and plug;
- a data processing circuit board the data processing circuit board includes a socket, an ADC analog-to-digital conversion chip, a microprocessor MCU, and a communication port.
- the socket is matched with the plug and is connected to the socket through the plug.
- the ADC analog-to-digital conversion chip is connected to the signal amplifier chip and the microprocessor MCU, and the microprocessor MCU is connected to the The terminal equipment is connected.
- it further includes:
- a thermal cycler the thermal cycler includes an end cover and a base, the end cover is movably mounted on the top of the base;
- the base includes a placement cavity for accommodating the microwell array chip, close to A heat conduction block provided at the bottom of the placement cavity, a temperature sensor placed at the upper end of the heat conduction block close to the placement cavity, a heater placed at the bottom of the heat conduction block, and a heater placed at the bottom of the heater Radiator;
- the two sides of the heat conduction block are fixed in the base by a limit plate, the heater is fixed at the bottom of the heat conduction block by a positioning plate, the temperature sensor and the heater are connected with each other through a control circuit
- the main control board is connected.
- the present invention also proposes a method for amplification using the digital PCR amplification device of the previous embodiment.
- the method includes:
- the present invention also proposes a method for performing amplification using the digital PCR amplification device of the previous embodiment.
- the method includes:
- microwell array chip after the PCR amplification reaction is cleaned, it is placed in a reading device, and the standard solution is added to the microwell, and then the target electrical signal of the microwell array chip is read;
- step (5) is performed according to the following steps:
- the capture probe of the biochemical sensor does not capture the target nucleic acid, and the difference between the biochemical sensor in the microwell before and after the PCR amplification reaction
- the value of the electrical signal is 0, and the wells that have not undergone PCR amplification are negative reaction units;
- the capture probe of the biochemical sensor captures the target nucleic acid, and the biochemical sensor in the micropore before and after the PCR amplification reaction
- the value of the difference electrical signal is the first electrical signal, and the microwell where a single amplification reaction of the DNA sample occurs is a positive reaction unit;
- the PCR amplification reaction occurs for a plurality of the DNA samples in the micropore;
- step (5-2) is performed according to the following steps:
- step (5-1) After the DNA sample with the concentration to be tested is subjected to the PCR amplification reaction, first calculate the number of all the positive reaction units on the microwell array chip according to step (5-1), and then draw Calculate the initial concentration of the DNA sample from the standard curve.
- step (5-2) is performed according to the following steps:
- the number of positive reaction units or the number of negative reaction units obtained by the histogram analysis is taken into the Poisson equation to calculate the initial concentration of the DNA sample.
- FIG. 1 is a schematic diagram of the body structure of a microwell array chip according to an embodiment of the present invention
- Fig. 2 (a) a schematic structural diagram of a chip holder type reading device according to an embodiment of the present invention (a perspective view in a closed state);
- FIG. 2 (b) a schematic structural diagram of a chip holder type reading device according to an embodiment of the present invention (a top view of a closed state);
- Fig. 2 (c) a schematic structural diagram of a chip holder type reading device according to an embodiment of the present invention (closed state front view);
- Fig. 2 (d) a schematic structural diagram of a chip holder type reading device according to an embodiment of the present invention (side view in an open state);
- Fig. 2 (e) a schematic structural diagram of a chip holder type reading device according to an embodiment of the present invention (a perspective view in an open state);
- FIG. 2 is a cross-sectional view taken along the line A-A in (c) in FIG. 2;
- FIG. 3 is a block diagram of the composition of a chip holder type reading device according to an embodiment of the present invention.
- Fig. 4 (a) is a schematic diagram of the overall structure of the card reader according to the embodiment of the present invention.
- FIG. 4 (b) is a schematic diagram of the structure of the card circuit board in the card reader device of the embodiment of the present invention.
- Fig. 5 is a block diagram of the composition of the card reader according to the embodiment of the present invention.
- Figure 6 is a schematic structural diagram of a thermal cycler according to an embodiment of the invention.
- Fig. 7 is a three-dimensional schematic diagram of a thermal cycler according to an embodiment of the present invention.
- FIG. 8 is a schematic diagram of method (1) of semiconductor chip micropore PCR in an embodiment of the present invention.
- FIG. 9 is a schematic diagram of method (2) of semiconductor chip micropore PCR in an embodiment of the present invention.
- Fig. 10 (a) a schematic diagram of the PCR machine adapter of the embodiment 1 of the present invention.
- FIG. 10(b) is a schematic cross-sectional view of the PCR machine adapter of FIG. 10(a);
- FIG. 10(c) is a partial enlarged schematic diagram of the PCR machine adapter in FIG. 10(b);
- Fig. 11 is a digital two-dimensional thermodynamic diagram of exemplary data of embodiment 1 of the present invention.
- Figure 12 The electrical signal changes (I/V curve) before and after DNA probe connection (ie, before and after surface chemistry) of Example 1 of the present invention
- Example 13 is a histogram of sensor signal changes before and after PCR amplification in Example 1 of the present invention.
- Fig. 14 is a graph of electrical signal changes (I/V curve) of positive units before and after PCR in Example 1 of the present invention.
- Figure 15 is a standard curve diagram of the number of positive units and the DNA concentration in Example 1 of the present invention.
- the present invention provides a digital PCR amplification device based on a microwell array chip.
- the digital PCR amplification device includes: a microwell array chip, and the microwell array chip includes:
- a biochemical sensor one biochemical sensor is arranged in each microwell 112 in the microwell array 111, and a capture probe 131 is arranged on the surface of the biochemical sensor, and the capture probe is suitable for capturing the microwell
- the biochemical sensor of the digital PCR amplification device of the above-mentioned embodiment of the present invention captures the amplified target nucleic acid molecules by providing capture probes on its surface, and replaces fluorescence with the electronic detection method that detects the inherent negative charge of the nucleic acid molecules.
- the above-mentioned device of the present application can significantly reduce the complexity, volume and price of the system.
- the present invention can greatly reduce the volume of micropores (which can be reduced to 1 fL to 10 pL), thereby significantly reducing the minimum reagent usage and the price of consumables.
- the electrode includes at least one of an on-chip electrode 141, a solution electrode 142 and an external electrode 143, wherein the on-chip electrode 141 or the solution electrode 142 is disposed on the bottom plate 110.
- the on-chip electrode 141 or the solution electrode 142 is disposed on the bottom plate 110.
- the microwell array 111 contains 10,000 to 10 million microwells 112, and the volume of each microwell 112 is 1fl-10pL.
- the sealing cover 120 is used for compression and sealing, so that the liquids in different micropores 112 are isolated from each other, and there is one target nucleic acid molecule in each micropore 112, thereby realizing single-molecule PCR amplification of DNA samples.
- the biochemical sensor may be one of an ion sensitive field effect transistor (ISFET), nanowire, graphene, or molybdenum disulfide transistor sensor, or a miniature electrochemical sensor.
- ISFET ion sensitive field effect transistor
- biochemical sensors sample a new type of nanowire as the channel field effect transistor nanowire FET or graphene or molybdenum disulfide and other two-dimensional semiconductor materials as the channel FET.
- these nanotransistor sensors can provide higher Sensitivity, thereby providing a smaller reaction chamber, higher integration and accuracy; miniature electrochemical sensors can greatly reduce the production cost of the amplification device.
- an ion sensitive field effect transistor includes a metal floating gate structure 132, a channel 133, a source electrode 134, a drain electrode 135 and a silicon substrate 136.
- ISFET ion sensitive field effect transistor
- the surface of the biochemical sensor is provided with a passivation layer 150 formed on the inner wall of the microhole 112, and the capture probe 131 is connected to the surface of the passivation layer on.
- the surface area of the biochemical sensor you can set at least one capture probe and a maximum of 1 million capture probes.
- nanowires can be coated with one to dozens of capture probes; if it is a relatively large surface area, such as a micropore area 2 A micrometer can be coated with thousands of capture probes.
- the method of connecting the capture probe 131 to the surface of the passivation layer can adopt a surface chemistry method to connect the capture probe to the surface of the passivation layer.
- the sulfhydryl DNA probe is directly connected to the surface of the passivation layer.
- biotin biotin
- avidin avidin
- Capture probes can also be formed firmly on the surface of the passivation layer; in other embodiments, an amine group is attached to one end of the DNA, and then the amine group is combined with a single molecule coated with an aldehyde group on the microporous array chip , So as to be fixed to the surface of the passivation layer.
- the passivation layer can not only prevent the solution in the micropores from contacting other structures such as the biochemical sensor, ensure the accuracy of the test, and prevent the metal material surface in the biochemical sensor from being corroded by the solution; moreover, the passivation layer can also be used for bearing Capture probe.
- the passivation layer 150 is a stack of one or more of gold, aluminum oxide, hafnium oxide, titanium dioxide, tantalum pentoxide, silicon dioxide, and silicon carbide. Therefore, the passivation layer does not react with the solution.
- the digital PCR amplification device of the above embodiment of the present invention further includes: a reading device, which is electrically connected to a computer, so as to realize the biochemical sensor in the microwell before and after the PCR amplification of the microwell array chip Reading of electrical signals.
- the reading device may be a chip holder-type reading device 200 based on a chip holder, and the chip holder-type reading device 200 specifically includes: The base 210, the circuit board 220 and the upper cover 230.
- the circuit board 220 is arranged on the lower surface of the base 210, and one side edge of the upper cover is hinged to the edge of the base to cover the base.
- a groove 211 for accommodating the microwell array chip 100 is formed on the upper surface of the base 210, and a metal probe 212 is provided in the bottom wall of the groove 211, and the metal probe 212 is suitable for contacting with
- the pin pads of the micropore array chip are electrically connected, so as to realize the power supply to the micropore array chip 100 and the data reading of the electrical signals of the biochemical sensor 130;
- the circuit board 220 includes a data acquisition module, an ADC chip, and a processor (not shown) connected in sequence, wherein the data acquisition module is connected to the metal probe and is suitable for collecting the biochemical
- the electrical signal of the sensor is transmitted to the ADC chip, and the ADC chip performs analog-to-digital conversion; the electrical signal after the analog-to-digital conversion is transmitted to the processor, and the processor Perform digital signal processing and calculate the concentration of amplified DNA.
- the processor of the circuit board 220 may be FPGA, DSP, or ARM.
- the reader may be a card reader based on a card chip PCB circuit board
- the device 300 specifically includes a card circuit board 310 and a data processing circuit board 320.
- the card plug-in circuit board 310 includes a container 311 for accommodating a microwell array chip, a cover 312 placed at the mouth of the container, and a signal for amplifying the biochemical sensor 130 on the microwell array chip 100.
- the pins of the biochemical sensor 130 are soldered on the card circuit board 310 to realize the circuit connection of the biochemical sensor 130.
- the signal amplifier chip 313 amplifies the electrical signal output by the biochemical sensor 130 to improve the signal-to-noise ratio.
- the ADC analog-to-digital conversion chip 322 transmitted to the data processing circuit board 320;
- the data processing circuit board 320 includes a socket 321, an ADC analog-to-digital conversion chip 322, a microprocessor MCU323, and a communication port.
- the socket 321 is matched with the plug 314, and is connected to the socket through the plug 314.
- the connection of 321 realizes the communication between the plug-in card circuit board 310 and the data processing circuit board 320.
- the ADC analog-to-digital conversion chip 322 is connected to the signal amplifier chip 313 and the microprocessor MCU323 respectively, and the microprocessor MCU323 passes through the communication port.
- the communication port may include the USB port 324, the serial port 325, or the parallel port 326 shown in (b) of FIG. 4.
- the terminal device can be a computer or a smart phone.
- the digital PCR amplification device of the foregoing embodiment of the present invention may further include a thermal cycler 400.
- the microwell array chip 100 can be placed on the thermal cycler 400 to perform the amplification reaction.
- the thermal cycler 400 includes an end cover 410 and a base, the end cover 410 is movably mounted on the top of the base;
- the base includes a placement cavity 420 for accommodating the microwell array chip body 100, a tight A heat conduction block 430 disposed at the bottom of the placement cavity 420, a temperature sensor 440 disposed at the upper end of the heat conduction block 430 at a position close to the placement cavity 420, a heater 450 placed at the bottom of the heat conduction block 430, and
- the temperature sensor 440 and the heater 450 are connected to the main control board 490 through a control circuit.
- the main control board 490 sets the temperature in the placement cavity 420 according to the needs of the PCR amplification reaction.
- the temperature sensor 440 is used to monitor the temperature in the placement cavity 420 and transmit it to the main control board 490.
- the actual temperature in 420 sends a heating or stopping command to the heater 450; the heater 450 may be a semiconductor heater or a thermal resistance.
- the present invention also proposes a method for amplification using the digital PCR amplification device of the previous embodiment.
- the method (1) includes:
- the above step (1) adding samples specifically includes: diluting or concentrating the target DNA fragment 3 according to the concentration in its original sample to a certain ratio, and then adding 5 pairs of primers and an amplification enzyme 4
- the buffer solution is mixed uniformly and then added to the micropores 112 on the micropore array chip, and is tightly sealed with the sealing cover 120.
- Each micropore 112 forms a mutually isolated PCR reaction unit, as shown in FIG. 8.
- Step (3) amplification specifically includes: Step (1)
- the microwell array chip 100 after sample loading can perform constant temperature PCR and variable temperature PCR amplification reactions, such as placing the microwell array chip 100 in a variable temperature PCR machine or a thermal cycler Variable temperature PCR amplification reaction can be realized on the 400, and the microwell array chip 100 can be placed on a constant temperature PCR machine or a constant temperature table to realize a constant temperature PCR amplification reaction; the sealed microwell array chip 100 can be placed on a PCR machine or a thermal cycler
- the PCR amplification reaction is carried out in the container; the target DNA fragment 3 in each microwell 112 is subjected to the chain PCR amplification reaction under the action of the primer pair 5 and the amplification enzyme 4, the copy number continues to increase, and is continuously captured and probed.
- the needle recognizes the capture and releases the electrical signal at the same time.
- the PCR machine is a flat-plate PCR or a PCR adapter is used for amplification in a traditional PCR machine, such as a 96-well plate.
- Step (4) The signal reading specifically includes: placing the body of the microwell array chip after PCR amplification reaction in the groove of the reading device, reading the electrical signal of the biochemical sensor at the bottom of the microwell, and obtaining the expansion after data processing.
- the increased DNA concentration is displayed on the computer or display screen.
- the upper cover is first opened, the body of the microwell array chip in the sealed state after the PCR amplification reaction is put into the groove on the base, and the upper cover is covered so that the sealed cover compresses the microwells; the microwell array chip
- the pin pad of the biochemical sensor at the bottom of the main body is electrically connected with the probe in the base, and then the probe is connected to the circuit board to supply power to the main body of the microwell array chip; then the data acquisition module collects the electric power of the biochemical sensor at the bottom of the microwell
- the signal is converted by the ADC chip, it is sent to FPGA, DSP, ARM and other processors for digital signal calculation processing, and then the calculated initial concentration of the DNA sample is sent to the display screen for display.
- step (5) is performed according to the following steps:
- step (5-2) is performed according to the following steps:
- step (5-1) After the DNA sample with the concentration to be tested is subjected to PCR amplification reaction, first calculate the number of all positive reaction units on the microwell array chip according to step (5-1), and then calculate the DNA sample's value according to the pre-drawn standard curve The initial concentration.
- step (5-2) can also be performed according to the following steps:
- the number of positive reaction units or the number of negative reaction units obtained from the histogram analysis is taken into the Poisson equation to calculate the initial concentration of the DNA sample.
- the present invention also proposes a method for performing amplification using the digital PCR amplification device of the previous embodiment.
- the method (2) includes:
- step (5) in the method (2) is the same as the operation analysis step in the step (5) in the method (1) described above, and will not be repeated here.
- the microporous array chip body with CMOS ISFET as a biochemical sensor is used as an example for specific description.
- the specific indicators are shown in Table 1:
- Detection of PCR signal type The hydrogen ion concentration, or the charge of the amplified DNA
- the operation of connecting the capture probe (also called DNA probe) to the microwell array chip is as follows: a. Mix the connection solution containing the capture probe (see Table 2) and add 2.5uL dropwise to the chip B. Put the microwell array chip into a vacuum device to vacuum (0.1M Pa) and keep it for 1 minute before taking it out; c. After keeping it at room temperature for 1 hour, wash off the unconnected capture probe with deionized water.
- microwell array chip 100 (also referred to as the chip) into the PCR cone adapter shown in Figure 10; d.
- the sealing cover seals the surface of the semiconductor chip and closes the PCR adapter upper cover 1030, and presses and seals the sealing sheet with the upper surface of the micropores of the micropore array chip 100, so that each micropore of the micropore array chip 100 is an independent reaction space.
- PCR tapered adapters can be individually or multiplely placed in the heating tank of the PCR instrument for heating. Liquid for PCR amplification; PCR tapered adapter has good thermal conductivity, which can quickly conduct heat from the heating tank of the PCR instrument to the chip; the chip can be detachably set on the PCR tapered adapter, so that the chip PCR adapter can complete different chips PCR amplification.
- the PCR cone adapter includes: a base 1010, an upper cover 1030, a plug 1040, a buckle 1060, and a spring 1070. Specifically: an upper cover 1030 buckled and connected to the base 1010 is provided on the upper cover 1030.
- the plug 1040 on the chip and the outer side of the upper cover 1030 are provided with a buckle 1060 that is buckled on the base.
- the middle of the buckle 1060 is pivotally connected to the upper cover 1030, the upper end of the buckle 1060 is fixedly connected to one end of the spring 1070, and the other end of the spring 1070 is fixed to the upper cover 1030.
- the adapter base is made of metal or thermal conductive material to conduct heat conduction on the chip body for PCR amplification.
- the amplification conditions are shown in Table 4 Shown:
- Method a Take out the chip and place it in In the socket of the reading device shown in Figures 2 and 3, the circuit of the reading device (provided the reference voltage for the micropore solution of the chip through the on-chip electrode) is directly connected to the chip pins, and the electrical signals of all the sensors in the micropores After data processing, it is read out to the computer or to the display screen; in order to prevent the change of the PCR solution after the PCR amplification in method a, two signals may occur, one is the charge signal of the DNA itself, and the other is the PCR solution itself Another false signal caused by the change, which leads to inaccurate measurement results.
- each time point 260,000 data are generated, as a frame, corresponding to 26 biochemical sensors.
- the data is 512 rows ⁇ 512 columns to form a two-dimensional heat map, as shown in Figure 11, the color of each pixel corresponds to the size of the output signal of the corresponding sensor, that is, the pH value/DNA charge in the corresponding micropore.
- Multiple time points can generate multiple frames of two-dimensional heat maps.
- (1) Before and after DNA probe connection First, obtain several frames of two-dimensional heat map data of the chip before and after DNA probe connection, and compare the multiple frames of electrical signals before and after DNA probe connection in the microwell. As shown in Fig. 12, the electrical signal of the microwell changes significantly, that is, the DNA probe is connected in the microwell.
- the upper curve A1 in Fig. 12 indicates before the DNA probe is connected, and the lower curve A2 indicates after the DNA probe is connected.
- the number of positive sensors calculated based on the signal of the sample to be tested on the chip body is brought into the standard curve equation to calculate the initial copy concentration (C2) of the DNA sample.
- the measured DNA copy concentration C2 is closer to the actual copy concentration C1, thus verifying that the obtained standard curve is consistent with the Poisson distribution formula.
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Abstract
Description
传感器种类 | ISFET |
微孔及传感器数量 | ~26万个 |
微孔尺寸(长,宽,深度) | 2微米,2微米,1.5微米 |
传感器表面感应材料种类 | Ta 2O 5/Au |
传感器表面感应材料厚度 | 20nm |
检测PCR的信号类型 | 氢离子浓度,或扩增后DNA的电荷 |
NaCl | 1M |
Tris-HCl | 50mM |
巯基PEG4 | 1mM |
TCEP | 1mM |
巯基DNA探针 | 10uM |
pH | 7.5 |
DNA Template | 0.01pM到1nM |
PCR MIX | 5ul |
Primer | 适量 |
去离子H 2O | 至10ul |
Claims (15)
- 一种基于微孔阵列芯片的数字PCR扩增装置,其特征在于,包括:微孔阵列芯片,所述微孔阵列芯片包括:底板,所述底板上形成有微孔阵列;密封盖,所述密封盖置于所述底板上方,用于密封所述微孔阵列中的每个微孔;多个生化传感器,所述微孔阵列中每个微孔内均设置有一个所述生化传感器,所述生化传感器表面上设置有捕获探针,所述捕获探针适于捕获所在微孔内的目标核酸;电极,所述电极适于向所述微孔内的溶液提供电压。
- 根据权利要求1所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,所述电极包括片上电极、溶液电极和外接电极中的至少一种,其中,所述片上电极或所述溶液电极设置在所述底板上。
- 根据权利要求1所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,所述生化传感器为离子敏感场效应晶体管,碳纳米管,硅纳米线、石墨烯或二硫化钼晶体管传感器中的一种,或微型电化学传感器。
- 根据权利要求1所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,所述生化传感器表面上设有钝化层,所述钝化层形成在所述微孔的内壁上,所述捕获探针设置在所述钝化层的表面上。
- 根据权利要求1或3所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,所述钝化层为金、三氧化二铝、二氧化铪、二氧化钛、五氧化二钽、二氧化硅、碳化硅中的一种或多种的叠加。
- 根据权利要求1或3所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,每个所述生化传感器表面上设置有1-100万个所述捕获探针。
- 根据权利要求1所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,还包括:读取装置,所述读取装置与计算机电气连接,以便实现所述微孔阵列芯片PCR扩增前及PCR扩增后所述微孔内的所述生化传感器电信号的读取。
- 根据权利要求7所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,所述读取装置包括:底座,所述底座的上表面上形成有用于容纳所述微孔阵列芯片的凹槽,所述凹槽的底壁内设置有金属探针,所述金属探针适于与所述微孔阵列芯片的引脚pad形成电气连接,从而实现对微孔阵列芯片的供电及生化传感器电信号的数据读取;电路板,所述电路板设置在所述底座的下表面上,所述电路板包括依次相连的数据采集模块、ADC芯片和处理器,其中,所述数据采集模块与所述金属探针相连,且适于采集所述生化传感器的电信号;所述电信号被输送至所述ADC芯片,并由所述ADC芯片进行模数转换;经过所述模数转换的电信号被输送给所述处理器,由所述处理器进行数字信号处理并计算出扩增后DNA的浓度;上盖,所述上盖的一侧边缘铰接在所述底座的边缘处,用于封盖所述底座。
- 根据权利要求7所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,所述读取装置包括:插卡电路板,所述插卡电路板包括用于容纳微孔阵列芯片的容纳仓、置于容纳仓仓口的压盖、用于放大所述微孔阵列芯片上所述生化传感器信号的信号放大器芯片以及插头;数据处理电路板,所述数据处理电路板包括插槽、ADC模数转换芯片、微处理器MCU和通信端口,所述插槽与所述插头相配,通过所述插头与所述插槽的连接实现所述插卡电路板与所述数据处理电路板的通信,所述ADC模数转换芯片分别与所述信号放大器芯片和所述微处理器MCU相连,所述微处理器MCU通过通信端口和终端设备相连。
- 根据权利要求1所述的基于微孔阵列芯片的数字PCR扩增装置,其特征在于,进一步包括:热循环器,所述热循环器包括端盖和基座,所述端盖活动安装在所述基座的顶部;所述基座包括用于容纳所述微孔阵列芯片的放置腔、紧挨所述放置腔底部设置的导热块、设置在所述导热块上端部紧挨所述放置腔位置处的温度传感器、置于所述导热块底部的加热器、以及置于所述加热器底部的散热器;所述导热块两侧通过限位板固定在所述基座内,所述加热器通过定位板固定在所述导热块的底部,所述温度传感器和所述加热器通过控制电路与主控板相连。
- 一种利用权利要求1-10任一项所述数字PCR扩增装置进行扩增的方法,其特征在于,包括:(1)将DNA反应体系滴加到所述微孔阵列芯片中的每个微孔内,并用所述密封盖密封;(2)将加样后的所述微孔阵列芯片放入读写装置中,读出所述微孔阵列芯片的初始电信号;(3)将加样后的所述微孔阵列芯片置于热循环器上进行PCR扩增反应;(4)将所述PCR扩增反应后的微孔阵列芯片置于读取装置内,利用所述读取装置读取所述微孔底部生化传感器的目标电信号;(5)通过数据处理后获得所述DNA样本的初始浓度,并显示在终端设备上。
- 一种利用权利要求1-10任一项所述数字PCR扩增装置进行扩增的方法,其特征在于,包括:(1)将所述微孔阵列芯片放入读写装置中,再加入标准液到微孔后,读出所述微孔阵列芯片的初始电信号;(2)取出所述微孔阵列芯片并去掉所述标准液后,将DNA反应体系滴加到所述微孔阵列中的每个所述微孔内,并用所述密封盖密封;(3)将加样后的所述微孔阵列芯片置于热循环器上进行PCR扩增反应;(4)将所述PCR扩增反应后的微孔阵列芯片清洗后,置于读取装置内,再加入所述标准液到微孔后,读出所述微孔阵列芯片的目标电信号;(5)通过数据处理后获得所述DNA样本的初始浓度,并显示在终端设备上。
- 根据权利要求11或12所述的方法,其特征在于,步骤(5)按照下列步骤进行:(5-1)直方图分析:对于每一个传感器,用所述目标电信号减去所述初始电信号获得每个所述微孔内的PCR扩增反应前后的所述DNA电荷的差值电信号,再对所述差值电信号的数据进行所述直方图Histogram分析,从而获得所述差值电信号的分布峰:若某个所述微孔中没有发生PCR扩增反应,则所述生化传感器的捕获探针未捕获到目标核酸,则所述微孔内所述生化传感器在所述PCR扩增反应前后的所述差值电信号的值为0,未发生所述PCR扩增反应的微孔为阴性反应单元;若所述微孔中发生了单个DNA样本扩增反应,则所述生化传感器的捕获探针捕获到所述目标核酸,则所述微孔内所述生化传感器在所述PCR扩增反应前后的所述差值电信号的值为第一电信号值,发生单个所述DNA样本扩增反应的微孔为阳性反应单元;若所述微孔内的所述生化传感器输出值的绝对值大于所述第一电信号值的绝对值,则此微孔内为多个所述DNA样本发生所述PCR扩增反应;(5-2)所述DNA样本初始浓度的计算:由步骤(5-1)获得的所述阳性反应单元个数或所述阴性反应单元个数计算所述DNA样本的初始浓度。
- 根据权利要求13所述的方法,其特征在于,步骤(5-2)按照下列步骤进行:绘制标准曲线:根据各组所述DNA样本的浓度和对应的所述阳性反应单元个数N绘制标准曲线C=f(N);数据计算:将待测浓度的所述DNA样本进行所述PCR扩增反应后,首先根据步骤(5-1)计算所述微孔阵列芯片上所有的所述阳性反应单元数量,然后根据预先绘制的标准曲线计算得到所述DNA样本的初始浓度。
- 根据权利要求13所述的方法,其特征在于,步骤(5-2)按照下列步骤进行:将所述直方图分析获得的所述阳性反应单元个数或所述阴性反应单元个数带入泊松方程计算所述DNA样本的初始浓度。
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